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Autophagy is a highly conserved intracellular degradation pathway that breaks down damaged macromolecules and/or organelles. It is involved in plant development and senescence, as well as in biotic and abiotic stresses. However, the autophagy process and related genes are largely unknown in citrus. In this study, we identified 35 autophagy-related genes (<i>CsATGs—</i>autophagy-related genes (<i>ATGs</i>) of <i>Citrus sinensis</i>, Cs) in a genome-wide manner from sweet orange (<i>Citrus sinensis</i>). Bioinformatic analysis showed that these CsATGs were highly similar to <i>Arabidopsis</i> ATGs in both sequence and phylogeny. All the <i>CsATGs</i> were randomly distributed on nine known (28 genes) and one unknown (7 genes) chromosomes. Ten <i>CsATGs</i> were predicted to be segmental duplications. Expression patterns suggested that most of the <i>CsATG</i> were significantly up- or down-regulated in response to drought; cold; heat; salt; mannitol; and excess manganese, copper, and cadmium stresses. In addition, two <i>ATG18</i> members, <i>CsATG18a</i> and <i>CsATG18b</i>, were cloned from sweet orange and ectopically expressed in <i>Arabidopsis</i>. The <i>CsATG18a</i> and <i>CsATG18b</i> transgenic plants showed enhanced tolerance to osmotic stress, salt, as well as drought (<i>CsATG18a</i>) or cold (<i>CsATG18b</i>), compared to wild-type plants. These results highlight the essential roles of <i>CsATG</i> genes in abiotic stresses.